X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2V2Y 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2940.1 M sodium acetate pH 4.6, 15 %(W/V) PEG 20000
Crystal Properties
Matthews coefficientSolvent content
1.830

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.911α = 90
b = 59.686β = 90
c = 88.443γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2015-03-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.937.498.40.05112.52.8624410
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.92.0196.70.490.791.892.81

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2V2Y1.937.423182121899.410.17890.176540.22474RANDOM41.434
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.321.2-1.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.952
r_dihedral_angle_4_deg16.964
r_dihedral_angle_3_deg13.701
r_long_range_B_refined6.113
r_long_range_B_other6.065
r_dihedral_angle_1_deg6.056
r_scangle_other3.281
r_mcangle_it2.225
r_mcangle_other2.224
r_scbond_it2.082
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.952
r_dihedral_angle_4_deg16.964
r_dihedral_angle_3_deg13.701
r_long_range_B_refined6.113
r_long_range_B_other6.065
r_dihedral_angle_1_deg6.056
r_scangle_other3.281
r_mcangle_it2.225
r_mcangle_other2.224
r_scbond_it2.082
r_scbond_other2.081
r_angle_refined_deg1.537
r_mcbond_other1.435
r_mcbond_it1.434
r_angle_other_deg1.411
r_chiral_restr0.087
r_bond_refined_d0.012
r_gen_planes_refined0.009
r_bond_other_d0.008
r_gen_planes_other0.007
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2439
Nucleic Acid Atoms
Solvent Atoms136
Heterogen Atoms21

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling